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<meta name="author" content="Chen Tong" />
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<li class="chapter" data-level="" data-path="index.html"><a href="index.html"><i class="fa fa-check"></i>Overview of BIC</a></li>
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<div id="analysis" class="section level1 hasAnchor" number="3">
<h1><span class="header-section-number">3</span> Analysis<a href="analysis.html#analysis" class="anchor-section" aria-label="Anchor link to header"></a></h1>
<div id="wgcna" class="section level2 hasAnchor" number="3.1">
<h2><span class="header-section-number">3.1</span> <a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MTY%3D%27">WGCNA</a><a href="analysis.html#wgcna" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, we used the gene expression table in different samples and the trait data of samples.</p>
<p>In the analysis parameters:</p>
<ul>
<li><p>Specify Bicor to calculate the correlation by selecting the option <code>Bicor</code> in the <code>Aorrelation algorithms</code> parameter;</p></li>
<li><p>Ahoose a type of network by selecting the option <code>Signed</code> in the <code>Network type</code> parameter;</p></li>
<li><p>Specify 30 to check by inputting <code>30</code> in the textarea of <code>Specify maximum power to check</code> parameter;</p></li>
<li><p>Pick the top 2000 genes with the biggest difference between samples to analyse by inputting <code>2000</code> in the textarea of <code>Only select top genes with maximum variances</code> parameter;</p></li>
<li><p>Remove outlier samples by selecting <code>TRUE</code> in the textarea of <code>Remove outlier samples</code> parameter;</p></li>
<li><p>Specify -2.5 as the threshold for judging abnormal samples by inputting <code>-2.5</code> in the textarea of <code>Outlier sample detection threshold</code> parameter;</p></li>
<li><p>Specify 0.85 to define scale-free network by inputting <code>2</code> in the textarea of <code>R square cut</code> parameter;</p></li>
<li><p>Detect the module whose size is lower than 25 by inputting <code>25</code> in the textarea of <code>Minimum module size for module detection</code> parameter;</p></li>
<li><p>Specify 2 to split module by inputting <code>2</code> in the textarea of <code>Deep split</code> parameter;</p></li>
<li><p>Set a random number to ensure that the result is repeatable by inputting <code>2020</code> in the <code>Seed for random number generator</code> parameter.</p></li>
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<div id="de-analysis-limma" class="section level2 hasAnchor" number="3.2">
<h2><span class="header-section-number">3.2</span> <a href="http://www.ehbio.com/Cloud_Platform/front/#/analysis?page=b%27MjU%3D%27">DE analysis (limma)</a><a href="analysis.html#de-analysis-limma" class="anchor-section" aria-label="Anchor link to header"></a></h2>
<p>In the demo1, we used the raw reads count table in different samples and the metadata of samples.</p>
<p>In the analysis parameters:</p>
<ul>
<li>Specify the type of input data by selecting the option <code>Raw reads count</code> in the <code>Expression data type</code> parameter;</li>
<li>Specify the column containing group information by selecting the option <code>conditions</code> in the <code>Group</code> parameter;</li>
<li>Remove outlier samples by selecting <code>TRUE</code> in the textarea of <code>Detect and remove outlier samples</code> parameter;</li>
<li>Do not detect and remove batch effect by selecting <code>False</code> in the textarea of <code>Detect and remove outlier samples</code> parameter;</li>
<li>The threshold is 1 and -1 of Log2 Fold change by inputting <code>1</code> in the textarea of <code>Log2 Fold change</code> parameter;</li>
<li>The threshold is 0.05 of FDR by inputting <code>0.05</code> in the textarea of <code>False discovery rate</code> parameter.</li>
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